jbrowse-plugin-graphgenomeviewer 8.2.0 → 8.3.1

package/dist/chunks/{chunk-IK3MQ4ZJ.js → chunk-NAC3EXT4.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-IK3MQ4ZJ.js.map
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+//# sourceMappingURL=chunk-NAC3EXT4.js.map

package/dist/chunks/{chunk-IK3MQ4ZJ.js.map → chunk-NAC3EXT4.js.map}

@@ -1,6 +1,6 @@
 {
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-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BEUTROKU.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BRH73RCH.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BEUTROKU.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BRH73RCH.js"],
   "sourcesContent": ["// src/util/groups.ts\nfunction pushTo(map, key, value) {\n  const list = map.get(key);\n  if (list) {\n    list.push(value);\n  } else {\n    map.set(key, [value]);\n  }\n}\nfunction addTo(map, key, value) {\n  const set = map.get(key);\n  if (set) {\n    set.add(value);\n  } else {\n    map.set(key, /* @__PURE__ */ new Set([value]));\n  }\n}\nfunction groupBy(items, keyOf) {\n  const groups = /* @__PURE__ */ new Map();\n  for (const item of items) {\n    pushTo(groups, keyOf(item), item);\n  }\n  return groups;\n}\n\nexport {\n  pushTo,\n  addTo,\n  groupBy\n};\n", "// src/util/partitionPoint.ts\nfunction partitionPoint(n, pred) {\n  let lo = 0;\n  let hi = n;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (pred(mid)) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\n\nexport {\n  partitionPoint\n};\n", "import {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/anchoredNodes.ts\nvar REFERENCE_RANK = 0;\nfunction isAnchored(node) {\n  return node.stable !== void 0;\n}\nfunction isBackbone(node) {\n  return node.stable?.rank === REFERENCE_RANK;\n}\nfunction isOffReference(node) {\n  return node.stable !== void 0 && node.stable.rank > REFERENCE_RANK;\n}\nfunction backboneNodes(graph) {\n  return graph.nodes.filter(isBackbone);\n}\nfunction overlapsWindow(node, window) {\n  return node.stable.start < window.end && node.stable.start + node.length > window.start;\n}\nfunction backbonePositions(backbone) {\n  const positions = {};\n  for (const node of backbone) {\n    positions[node.id] = [\n      { x: node.stable.start, y: 0 },\n      { x: node.stable.start + node.length, y: 0 }\n    ];\n  }\n  return positions;\n}\nfunction firstNodeAtOrAfter(nodes, bp) {\n  return partitionPoint(nodes.length, (i) => nodes[i].stable.start < bp);\n}\nfunction backboneSpan(backbone) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const node of backbone) {\n    min = Math.min(min, node.stable.start);\n    max = Math.max(max, node.stable.start + node.length);\n  }\n  return max - min;\n}\nfunction referenceSpan(backbone, region) {\n  return region && region.end > region.start ? region.end - region.start : backboneSpan(backbone);\n}\n\nexport {\n  REFERENCE_RANK,\n  isAnchored,\n  isBackbone,\n  isOffReference,\n  backboneNodes,\n  overlapsWindow,\n  backbonePositions,\n  firstNodeAtOrAfter,\n  backboneSpan,\n  referenceSpan\n};\n", "// src/pathVisits.ts\nvar PathVisits = class {\n  constructor(columns) {\n    this.segments = columns.segments;\n    this.offsets = columns.offsets;\n    this.path = columns.path;\n    this.start = columns.start;\n    this.reversed = columns.reversed;\n    this.paths = columns.paths;\n    this.samples = columns.samples;\n    this.slots = new Map(this.segments.map((s, i) => [s, i]));\n  }\n  static from(entries) {\n    const builder = new PathVisitsBuilder();\n    for (const [segment, visits] of entries) {\n      builder.declare(segment);\n      for (const v of visits) {\n        builder.add(segment, v.path, v.sample, v.start, v.strand === \"-\");\n      }\n    }\n    return builder.build();\n  }\n  get size() {\n    return this.segments.length;\n  }\n  // the segment's index into `segments` and `offsets`, -1 when unvisited\n  slot(segment) {\n    return this.slots.get(segment) ?? -1;\n  }\n  pathIndex(path) {\n    return this.paths.indexOf(path);\n  }\n  // the first of `slot`'s visits by path `p`, -1 for none\n  firstBy(slot, p) {\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      if (this.path[i] === p) {\n        return i;\n      }\n    }\n    return -1;\n  }\n  // the visit of `slot` on the path first in name order, at its lowest offset\n  // there: where gfa-to-tabix places a segment the reference doesn't visit, so\n  // both place it alike whatever order the file lists its paths in\n  firstByName(slot) {\n    let best = this.offsets[slot];\n    for (let i = best + 1; i < this.offsets[slot + 1]; i++) {\n      const a = this.paths[this.path[i]];\n      const b = this.paths[this.path[best]];\n      if (a < b || a === b && this.start[i] < this.start[best]) {\n        best = i;\n      }\n    }\n    return best;\n  }\n  // Paths' steps replayed in walk order against their visits: the k-th call\n  // for one path and segment answers that path's k-th visit there, -1 past\n  // its last. A walk in pieces lists its pieces in path order, so replaying\n  // the pieces in order reads each step's own visit.\n  replay() {\n    const cursor = /* @__PURE__ */ new Map();\n    return (slot, p) => {\n      if (slot < 0 || p < 0) {\n        return -1;\n      }\n      const key = slot * this.paths.length + p;\n      const end = this.offsets[slot + 1];\n      let at = cursor.get(key) ?? this.offsets[slot];\n      while (at < end && this.path[at] !== p) {\n        at++;\n      }\n      cursor.set(key, at + 1);\n      return at < end ? at : -1;\n    };\n  }\n  // the visits of paths `keepPath` accepts, at segments `keepSegment` does\n  filter(keepPath, keepSegment = () => true) {\n    const kept = this.paths.map(keepPath);\n    const builder = new PathVisitsBuilder();\n    this.segments.forEach((segment, s) => {\n      if (!keepSegment(segment)) {\n        return;\n      }\n      const slot = builder.declare(segment);\n      for (let i = this.offsets[s]; i < this.offsets[s + 1]; i++) {\n        const p = this.path[i];\n        if (kept[p]) {\n          builder.addAt(\n            slot,\n            builder.pathOf(this.paths[p], this.samples[p]),\n            this.start[i],\n            this.reversed[i] === 1\n          );\n        }\n      }\n    });\n    return builder.build();\n  }\n  strand(i) {\n    return this.reversed[i] ? \"-\" : \"+\";\n  }\n  visit(i) {\n    const p = this.path[i];\n    return {\n      path: this.paths[p],\n      sample: this.samples[p],\n      start: this.start[i],\n      strand: this.strand(i)\n    };\n  }\n  visitsAt(slot) {\n    const out = [];\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      out.push(this.visit(i));\n    }\n    return out;\n  }\n  get(segment) {\n    const slot = this.slot(segment);\n    return slot < 0 ? void 0 : this.visitsAt(slot);\n  }\n  has(segment) {\n    return this.slots.has(segment);\n  }\n  keys() {\n    return this.segments[Symbol.iterator]();\n  }\n  *values() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield this.visitsAt(s);\n    }\n  }\n  *entries() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield [this.segments[s], this.visitsAt(s)];\n    }\n  }\n  [Symbol.iterator]() {\n    return this.entries();\n  }\n};\nvar Column = class {\n  constructor(data) {\n    this.data = data;\n    this.length = 0;\n  }\n  push(value) {\n    if (this.length === this.data.length) {\n      const grown = new this.data.constructor(\n        this.data.length * 2\n      );\n      grown.set(this.data);\n      this.data = grown;\n    }\n    this.data[this.length++] = value;\n  }\n};\nvar PathVisitsBuilder = class {\n  constructor() {\n    this.segments = [];\n    this.slots = /* @__PURE__ */ new Map();\n    this.paths = [];\n    this.samples = [];\n    this.pathIndex = /* @__PURE__ */ new Map();\n    this.slot = new Column(new Int32Array(1024));\n    this.path = new Column(new Int32Array(1024));\n    this.start = new Column(new Float64Array(1024));\n    this.reversed = new Column(new Uint8Array(1024));\n  }\n  // a segment's place in iteration order, though it has no visits yet\n  declare(segment) {\n    let s = this.slots.get(segment);\n    if (s === void 0) {\n      s = this.segments.length;\n      this.slots.set(segment, s);\n      this.segments.push(segment);\n    }\n    return s;\n  }\n  // a path's index, so a caller adding many of its visits names it once\n  pathOf(path, sample) {\n    let p = this.pathIndex.get(path);\n    if (p === void 0) {\n      p = this.paths.length;\n      this.pathIndex.set(path, p);\n      this.paths.push(path);\n      this.samples.push(sample);\n    }\n    return p;\n  }\n  add(segment, path, sample, start, reversed) {\n    this.addAt(\n      this.declare(segment),\n      this.pathOf(path, sample),\n      start,\n      reversed\n    );\n  }\n  addAt(slot, path, start, reversed) {\n    this.slot.push(slot);\n    this.path.push(path);\n    this.start.push(start);\n    this.reversed.push(reversed ? 1 : 0);\n  }\n  build() {\n    const n = this.slot.length;\n    const segments = this.segments.length;\n    const offsets = new Int32Array(segments + 1);\n    const slot = this.slot.data;\n    for (let i = 0; i < n; i++) {\n      offsets[slot[i] + 1]++;\n    }\n    for (let s = 0; s < segments; s++) {\n      offsets[s + 1] += offsets[s];\n    }\n    const fill = offsets.slice(0, segments);\n    const path = new Int32Array(n);\n    const start = new Float64Array(n);\n    const reversed = new Uint8Array(n);\n    for (let i = 0; i < n; i++) {\n      const at = fill[slot[i]]++;\n      path[at] = this.path.data[i];\n      start[at] = this.start.data[i];\n      reversed[at] = this.reversed.data[i];\n    }\n    return new PathVisits({\n      segments: this.segments,\n      offsets,\n      path,\n      start,\n      reversed,\n      paths: this.paths,\n      samples: this.samples\n    });\n  }\n};\n\nexport {\n  PathVisits,\n  Column,\n  PathVisitsBuilder\n};\n", "import {\n  PathVisitsBuilder\n} from \"./chunk-BEUTROKU.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  REFERENCE_RANK\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathAnchoring.ts\nvar RANGE_SUFFIX = /:(\\d+)-\\d+$/;\nvar VG_FRAGMENT = /^([^#]*#[^#]*#[^#[]*)#(\\d+)(?:\\[(\\d+)-\\d+\\])?$/;\nvar VG_SUBRANGE = /\\[(\\d+)-\\d+\\]$/;\nfunction pathOrigin(pathName) {\n  const fragment = VG_FRAGMENT.exec(pathName);\n  if (fragment) {\n    return { name: fragment[1], start: +fragment[2] + +(fragment[3] ?? 0) };\n  }\n  const match = RANGE_SUFFIX.exec(pathName) ?? VG_SUBRANGE.exec(pathName);\n  return match ? { name: pathName.slice(0, match.index), start: +match[1] } : { name: pathName, start: 0 };\n}\nfunction surveyPaths(paths, lengthOf) {\n  const anchorPaths = [];\n  const visits = new PathVisitsBuilder();\n  for (const path of paths) {\n    const sample = panSNSample(path.name);\n    const p = visits.pathOf(path.name, sample);\n    let pos = path.start;\n    for (const step of path.steps) {\n      visits.addAt(visits.declare(step.id), p, pos, step.strand === \"-\");\n      pos += lengthOf(step.id);\n    }\n    anchorPaths.push({\n      name: path.name,\n      sample,\n      start: path.start,\n      length: pos - path.start\n    });\n  }\n  return { anchorPaths, pathVisits: visits.build() };\n}\nfunction chooseReferencePath(anchorPaths, preferred) {\n  const named = anchorPaths.find(\n    (p) => p.sample === preferred || p.name === preferred\n  );\n  return named ?? anchorPaths[0];\n}\nvar OFF_REFERENCE_RANK = 1;\nfunction anchorNode(node, visits, reference, samplesOf) {\n  const slot = visits.slot(node.name);\n  if (slot < 0 || visits.offsets[slot] === visits.offsets[slot + 1]) {\n    return node;\n  }\n  const own = visits.firstBy(slot, reference);\n  const anchor = own >= 0 ? own : visits.firstByName(slot);\n  return {\n    ...node,\n    stable: {\n      refName: visits.paths[visits.path[anchor]],\n      start: visits.start[anchor],\n      rank: own >= 0 ? REFERENCE_RANK : OFF_REFERENCE_RANK,\n      strand: visits.strand(anchor)\n    },\n    samples: samplesOf(slot)\n  };\n}\nfunction sampleSorter(visits) {\n  const sorted = [...new Set(visits.samples)].sort();\n  const rank = new Map(sorted.map((sample, i) => [sample, i]));\n  const pathRank = Int32Array.from(visits.samples, (s) => rank.get(s));\n  const seen = new Uint8Array(sorted.length);\n  const ranks = new Int32Array(sorted.length);\n  return (slot) => {\n    let n = 0;\n    for (let i = visits.offsets[slot]; i < visits.offsets[slot + 1]; i++) {\n      const r = pathRank[visits.path[i]];\n      if (seen[r] === 0) {\n        seen[r] = 1;\n        ranks[n++] = r;\n      }\n    }\n    let out;\n    if (n === sorted.length) {\n      out = sorted;\n      seen.fill(0);\n    } else if (n * 8 < sorted.length) {\n      const found = ranks.subarray(0, n);\n      found.forEach((r) => seen[r] = 0);\n      out = Array.from(found.sort(), (r) => sorted[r]);\n    } else {\n      out = [];\n      for (let r = 0; r < sorted.length; r++) {\n        if (seen[r] === 1) {\n          seen[r] = 0;\n          out.push(sorted[r]);\n        }\n      }\n    }\n    return out;\n  };\n}\nfunction anchorFromPaths(graph, preferred) {\n  const { anchorPaths, pathVisits } = graph;\n  const reference = anchorPaths && pathVisits ? chooseReferencePath(anchorPaths, preferred) : void 0;\n  if (!reference || !anchorPaths || !pathVisits) {\n    return graph;\n  }\n  const samplesOf = sampleSorter(pathVisits);\n  const referenceIndex = pathVisits.pathIndex(reference.name);\n  return {\n    ...graph,\n    nodes: graph.nodes.map(\n      (node) => anchorNode(node, pathVisits, referenceIndex, samplesOf)\n    ),\n    anchoredBy: \"paths\",\n    referencePath: reference.name\n  };\n}\nfunction anchorGraph(graph, preferred) {\n  if (graph.anchoredBy !== \"tags\") {\n    return anchorFromPaths(graph, preferred);\n  }\n  const referencePath = taggedReferencePath(graph);\n  return referencePath ? { ...graph, referencePath } : graph;\n}\nfunction taggedReferencePath(graph) {\n  const refName = graph.nodes.find((n) => n.stable?.rank === 0)?.stable?.refName;\n  return refName !== void 0 && graph.anchorPaths?.some((p) => p.name === refName) ? refName : void 0;\n}\nfunction trimOrigins(graph, kept) {\n  if (!graph.anchorPaths) {\n    return void 0;\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const bp = (ids, end = ids.length) => {\n    let sum = 0;\n    for (let i = 0; i < end; i++) {\n      sum += lengthOf.get(ids[i]) ?? 0;\n    }\n    return sum;\n  };\n  const byOrigin = groupBy(graph.paths ?? [], (p) => pathOrigin(p.name).name);\n  return graph.anchorPaths.map((o) => {\n    const pieces = byOrigin.get(o.name);\n    const path = pieces?.length === 1 ? pieces[0] : void 0;\n    const stretch = path && kept.get(path.name);\n    return path && stretch ? {\n      ...o,\n      start: o.start + bp(path.nodeIds, stretch.first),\n      length: bp(stretch.nodeIds)\n    } : o;\n  });\n}\nfunction referenceVisitStarts(graph) {\n  const { pathVisits } = graph;\n  const cache = /* @__PURE__ */ new Map();\n  return (node) => {\n    let starts = cache.get(node.id);\n    if (!starts) {\n      starts = [];\n      const slot = pathVisits ? pathVisits.slot(node.name) : -1;\n      const p = slot >= 0 ? pathVisits.pathIndex(node.stable.refName) : -1;\n      if (p >= 0) {\n        for (let i = pathVisits.offsets[slot]; i < pathVisits.offsets[slot + 1]; i++) {\n          if (pathVisits.path[i] === p) {\n            starts.push(pathVisits.start[i]);\n          }\n        }\n      }\n      if (starts.length < 2) {\n        starts = [node.stable.start];\n      }\n      cache.set(node.id, starts);\n    }\n    return starts;\n  };\n}\n\nexport {\n  pathOrigin,\n  surveyPaths,\n  chooseReferencePath,\n  anchorFromPaths,\n  anchorGraph,\n  trimOrigins,\n  referenceVisitStarts\n};\n"],
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package/dist/chunks/{chunk-CVHKXFVS.js.map → chunk-NSBH4FIW.js.map}

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curvePointAt(mid, 0.5) : void 0;\n}\nfunction curveBounds(curves) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const c of curves) {\n    minX = Math.min(minX, c.x0, c.cx0, c.cx1, c.x1);\n    maxX = Math.max(maxX, c.x0, c.cx0, c.cx1, c.x1);\n    minY = Math.min(minY, c.y0, c.cy0, c.cy1, c.y1);\n    maxY = Math.max(maxY, c.y0, c.cy0, c.cy1, c.y1);\n  }\n  return { minX, minY, maxX, maxY };\n}\nfunction subCurve(c, t0, t1) {\n  const p0 = curvePointAt(c, t0);\n  const p1 = curvePointAt(c, t1);\n  const dt = (t1 - t0) / 3;\n  const d0 = curveTangentAt(c, t0);\n  const d1 = curveTangentAt(c, t1);\n  return {\n    x0: p0.x,\n    y0: p0.y,\n    cx0: p0.x + d0.x * dt,\n    cy0: p0.y + d0.y * dt,\n    cx1: p1.x - d1.x * dt,\n    cy1: p1.y - d1.y * dt,\n    x1: p1.x,\n    y1: p1.y\n  };\n}\nfunction curveTangentAt(c, t) {\n  const u = 1 - t;\n  const a = 3 * u * u;\n  const b = 6 * u * t;\n  const d = 3 * t * t;\n  return {\n    x: a * (c.cx0 - c.x0) + b * (c.cx1 - c.cx0) + d * (c.x1 - c.cx1),\n    y: a * (c.cy0 - c.y0) + b * (c.cy1 - c.cy0) + d * (c.y1 - c.cy1)\n  };\n}\nvar VISIBLE_SAMPLES = 32;\nfunction visibleStretches(curves, lengths, bounds, yToX) {\n  const stretches = [];\n  let start = 0;\n  curves.forEach((c, k) => {\n    const length = lengths[k];\n    const pad = length / VISIBLE_SAMPLES;\n    let last = curvePointAt(c, 0);\n    for (let i = 1; i <= VISIBLE_SAMPLES; i++) {\n      const next = curvePointAt(c, i / VISIBLE_SAMPLES);\n      if (Math.max(last.x, next.x) + pad >= bounds.minX && Math.min(last.x, next.x) - pad <= bounds.maxX && Math.max(last.y, next.y) + pad / yToX >= bounds.minY && Math.min(last.y, next.y) - pad / yToX <= bounds.maxY) {\n        const from = start + length * (i - 1) / VISIBLE_SAMPLES;\n        const to = start + length * i / VISIBLE_SAMPLES;\n        const prev = stretches.at(-1);\n        if (prev && prev[1] >= from) {\n          prev[1] = to;\n        } else {\n          stretches.push([from, to]);\n        }\n      }\n      last = next;\n    }\n    start += length;\n  });\n  return stretches;\n}\nvar dashCurves = (curves, dashWorld, yToX = 1, bounds) => dashSpans(curves, dashWorld, yToX, bounds).map((d) => d.curves);\nfunction dashSpans(curves, dashWorld, yToX = 1, bounds) {\n  const lengths = curves.map(\n    (c) => Math.hypot(c.cx0 - c.x0, (c.cy0 - c.y0) * yToX) + Math.hypot(c.cx1 - c.cx0, (c.cy1 - c.cy0) * yToX) + Math.hypot(c.x1 - c.cx1, (c.y1 - c.cy1) * yToX)\n  );\n  const total = lengths.reduce((a, b) => a + b, 0);\n  const periods = Math.round(total / dashWorld);\n  const spans = Math.max(3, periods % 2 ? periods : periods + 1);\n  const stretches = bounds ? visibleStretches(curves, lengths, bounds, yToX) : void 0;\n  let seen = 0;\n  const out = [];\n  for (let i = 0; i < spans; i += 2) {\n    const from = i / spans * total;\n    const to = (i + 1) / spans * total;\n    if (stretches) {\n      while (seen < stretches.length && stretches[seen][1] < from) {\n        seen++;\n      }\n      if (seen === stretches.length) {\n        break;\n      }\n      if (stretches[seen][0] > to) {\n        continue;\n      }\n    }\n    const dash = [];\n    const along = [];\n    let start = 0;\n    curves.forEach((c, k) => {\n      const length = lengths[k];\n      const end = start + length;\n      if (length > 0 && end > from && start < to) {\n        const t0 = Math.max(0, (from - start) / length);\n        const t1 = Math.min(1, (to - start) / length);\n        dash.push(subCurve(c, t0, t1));\n        along.push((k + t0) / curves.length, (k + t1) / curves.length);\n      }\n      start = end;\n    });\n    if (dash.length) {\n      out.push({\n        curves: dash,\n        startAlong: along[0],\n        endAlong: along.at(-1)\n      });\n    }\n  }\n  return out;\n}\nvar slideAt = (from, to, along) => ({\n  dx: from.dx + (to.dx - from.dx) * along,\n  dy: from.dy + (to.dy - from.dy) * along\n});\nfunction slideCurves(curves, fromDx, fromDy, toDx, toDy) {\n  const n = curves.length;\n  const out = new Array(n);\n  for (let i = 0; i < n; i++) {\n    const c = curves[i];\n    const a = i / n;\n    const b = (i + 1) / n;\n    const adx = fromDx + (toDx - fromDx) * a;\n    const ady = fromDy + (toDy - fromDy) * a;\n    const bdx = fromDx + (toDx - fromDx) * b;\n    const bdy = fromDy + (toDy - fromDy) * b;\n    out[i] = {\n      x0: c.x0 + adx,\n      y0: c.y0 + ady,\n      cx0: c.cx0 + adx,\n      cy0: c.cy0 + ady,\n      cx1: c.cx1 + bdx,\n      cy1: c.cy1 + bdy,\n      x1: c.x1 + bdx,\n      y1: c.y1 + bdy\n    };\n  }\n  return out;\n}\nfunction translateCurves(curves, dx, dy) {\n  const out = new Array(curves.length);\n  for (let i = 0; i < curves.length; i++) {\n    const c = curves[i];\n    out[i] = {\n      x0: c.x0 + dx,\n      y0: c.y0 + dy,\n      cx0: c.cx0 + dx,\n      cy0: c.cy0 + dy,\n      cx1: c.cx1 + dx,\n      cy1: c.cy1 + dy,\n      x1: c.x1 + dx,\n      y1: c.y1 + dy\n    };\n  }\n  return out;\n}\nfunction attachment(segments, side) {\n  const last = segments.length - 1;\n  return side === \"end\" ? { at: segments[last], inward: segments[last - 1] } : { at: segments[0], inward: segments[1] };\n}\nvar TANGENT_SPAN_FACTOR = 0.5;\nvar MAX_TANGENT = 80;\nfunction ownStrand(id) {\n  return id.endsWith(\"-\") ? \"-\" : \"+\";\n}\nfunction strandSides(edge) {\n  const own = (id, strand) => (strand ?? ownStrand(id)) === ownStrand(id);\n  return {\n    from: own(edge.from, edge.fromStrand) ? \"end\" : \"start\",\n    to: own(edge.to, edge.toStrand) ? \"start\" : \"end\"\n  };\n}\nfunction spanOf(segments) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const s of segments) {\n    min = Math.min(min, s.x);\n    max = Math.max(max, s.x);\n  }\n  return { min, max };\n}\nfunction distanceToSpan(x, span) {\n  return Math.max(0, span.min - x, x - span.max);\n}\nfunction facingSide(segments, other, tieBreak) {\n  const startGap = distanceToSpan(segments[0].x, other);\n  const endGap = distanceToSpan(segments[segments.length - 1].x, other);\n  return startGap === endGap ? tieBreak : startGap < endGap ? \"start\" : \"end\";\n}\nfunction facingSides(fromSegments, toSegments) {\n  return {\n    from: facingSide(fromSegments, spanOf(toSegments), \"end\"),\n    to: facingSide(toSegments, spanOf(fromSegments), \"start\")\n  };\n}\nvar laidSides = /* @__PURE__ */ new WeakMap();\nfunction heldFacingSides(fromSegments, toSegments) {\n  let byTo = laidSides.get(fromSegments);\n  if (!byTo) {\n    byTo = /* @__PURE__ */ new WeakMap();\n    laidSides.set(fromSegments, byTo);\n  }\n  let sides = byTo.get(toSegments);\n  if (!sides) {\n    sides = facingSides(fromSegments, toSegments);\n    byTo.set(toSegments, sides);\n  }\n  return sides;\n}\nvar APEX_FRACTION = 0.75;\nvar BOW_CLEARANCE = 1.15;\nvar ALONG_FRACTION = 0.35;\nvar MAX_ROW_BOW_PX = 3 * ROW_HEIGHT_PX;\nfunction bowAround(p1x, p1y, p2x, p2y, toward, maxBow) {\n  const chord = Math.hypot(p2x - p1x, p2y - p1y);\n  const ux = chord === 0 ? 1 : (p2x - p1x) / chord;\n  const uy = chord === 0 ? 0 : (p2y - p1y) / chord;\n  let reach = 0;\n  let minAlong = Infinity;\n  let maxAlong = -Infinity;\n  for (const p of toward) {\n    const dx = p.x - p1x;\n    const dy = p.y - p1y;\n    const perp = dx * -uy + dy * ux;\n    if (Math.abs(perp) > Math.abs(reach)) {\n      reach = perp;\n    }\n    const along = dx * ux + dy * uy;\n    minAlong = Math.min(minAlong, along);\n    maxAlong = Math.max(maxAlong, along);\n  }\n  const span = toward.length ? maxAlong - minAlong : 0;\n  const uncapped = Math.max(\n    Math.abs(reach) * BOW_CLEARANCE / APEX_FRACTION,\n    span * ALONG_FRACTION\n  );\n  const size = maxBow === void 0 ? uncapped : Math.min(uncapped, maxBow);\n  return reach < 0 ? -size : size;\n}\nfunction yToXOf({ scaleX, scaleY }) {\n  return scaleY / scaleX;\n}\nvar PATH_RIBBON_SPACING_PX = 3;\nfunction drawnDirection(a, b, yToX) {\n  const dx = b.x - a.x;\n  const dy = (b.y - a.y) * yToX;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? void 0 : { x: dx / len, y: dy / len };\n}\nfunction pathRibbonOffsets(fromSegments, toSegments, count, axis) {\n  const yToX = yToXOf(axis);\n  const spacing = PATH_RIBBON_SPACING_PX / Math.max(axis.scaleX, 1e-6);\n  const dir = drawnDirection(\n    fromSegments[fromSegments.length - 1],\n    toSegments[0],\n    yToX\n  ) ?? drawnDirection(fromSegments[0], fromSegments.at(-1), yToX) ?? drawnDirection(toSegments[0], toSegments.at(-1), yToX) ?? { x: 1, y: 0 };\n  const offsets = [];\n  for (let i = 0; i < count; i++) {\n    const distance = (i - (count - 1) / 2) * spacing;\n    offsets.push({ x: -dir.y * distance, y: dir.x * distance / yToX });\n  }\n  return offsets;\n}\nfunction scaleYOf(points, yToX) {\n  return points.map((p) => ({ x: p.x, y: p.y * yToX }));\n}\nfunction unscaleYOf(curves, yToX) {\n  for (const c of curves) {\n    c.y0 /= yToX;\n    c.cy0 /= yToX;\n    c.cy1 /= yToX;\n    c.y1 /= yToX;\n  }\n  return curves;\n}\nfunction polylinePx(points, scaleX, scaleY) {\n  let total = 0;\n  for (let i = 1; i < points.length; i++) {\n    const a = points[i - 1];\n    const b = points[i];\n    total += Math.hypot((b.x - a.x) * scaleX, (b.y - a.y) * scaleY);\n  }\n  return total;\n}\nvar SELF_LOOP_MIN_PX = 12;\nvar SELF_LOOP_MAX_PX = 40;\nfunction selfLoopReach(segments, scale) {\n  const nodePx = polylinePx(segments, scale, scale);\n  const reachPx = Math.min(\n    SELF_LOOP_MAX_PX,\n    Math.max(SELF_LOOP_MIN_PX, nodePx / 2)\n  );\n  return reachPx / Math.max(scale, Number.EPSILON);\n}\nfunction selfLinkOf(edge) {\n  if (edge.from !== edge.to) {\n    return false;\n  }\n  return edge.fromStrand && edge.toStrand && edge.fromStrand !== edge.toStrand ? edge.fromStrand === \"+\" ? \"end\" : \"start\" : true;\n}\nfunction edgeJoinOf(edge, stranded = false) {\n  const self = selfLinkOf(edge);\n  if (!stranded) {\n    return self;\n  }\n  const sides = strandSides(edge);\n  return self === false ? sides : sides.from === sides.to ? sides.from : true;\n}\nfunction hairpinCurves(attach, reach) {\n  const { at, inward } = attach;\n  const dx = inward ? at.x - inward.x : 1;\n  const dy = inward ? at.y - inward.y : 0;\n  const len = Math.hypot(dx, dy) || 1;\n  const ux = dx / len;\n  const uy = dy / len;\n  const px = at.x;\n  const py = at.y;\n  const nearX = px + ux * reach / 3;\n  const nearY = py + uy * reach / 3;\n  const apexX = px + ux * reach;\n  const apexY = py + uy * reach;\n  const sideX = -uy * reach / 2;\n  const sideY = ux * reach / 2;\n  return [\n    {\n      x0: px,\n      y0: py,\n      cx0: nearX,\n      cy0: nearY,\n      cx1: apexX + sideX,\n      cy1: apexY + sideY,\n      x1: apexX,\n      y1: apexY\n    },\n    {\n      x0: apexX,\n      y0: apexY,\n      cx0: apexX - sideX,\n      cy0: apexY - sideY,\n      cx1: nearX,\n      cy1: nearY,\n      x1: px,\n      y1: py\n    }\n  ];\n}\nfunction computeEdgeCurves(fromSegments, toSegments, join, axis, bypassed = [], maxBowIn) {\n  const scale = axis.scaleX;\n  const yToX = yToXOf(axis);\n  const maxBow = maxBowIn ?? (axis.pixelRows ? MAX_ROW_BOW_PX : void 0);\n  if (join === false) {\n    join = heldFacingSides(fromSegments, toSegments);\n  }\n  if (yToX !== 1) {\n    return unscaleYOf(\n      computeEdgeCurves(\n        scaleYOf(fromSegments, yToX),\n        scaleYOf(toSegments, yToX),\n        join,\n        { scaleX: scale, scaleY: scale },\n        scaleYOf(bypassed, yToX),\n        // the cap is a y measure and the body works in x units, so it converts\n        // with everything else that crosses this boundary\n        maxBow === void 0 ? void 0 : maxBow * yToX\n      ),\n      yToX\n    );\n  }\n  if (typeof join === \"string\") {\n    return hairpinCurves(\n      attachment(fromSegments, join),\n      selfLoopReach(fromSegments, scale)\n    );\n  }\n  const loop = join === true;\n  const sides = join === true ? { from: \"end\", to: \"start\" } : join;\n  const fromAttach = attachment(fromSegments, sides.from);\n  const toAttach = attachment(toSegments, sides.to);\n  const fromEnd = fromAttach.at;\n  const toStart = toAttach.at;\n  const p1x = fromEnd.x;\n  const p1y = fromEnd.y;\n  const p2x = toStart.x;\n  const p2y = toStart.y;\n  if (loop) {\n    let segDirX = 1;\n    let segDirY = 0;\n    if (fromAttach.inward) {\n      const dx = fromEnd.x - fromAttach.inward.x;\n      const dy = fromEnd.y - fromAttach.inward.y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        segDirX = dx / len;\n        segDirY = dy / len;\n      }\n    }\n    const ext = selfLoopReach(fromSegments, scale);\n    const perpX = -segDirY;\n    const perpY = segDirX;\n    const midX = (fromEnd.x + toStart.x) / 2 + perpX * ext;\n    const midY = (fromEnd.y + toStart.y) / 2 + perpY * ext;\n    const cp1x = p1x + segDirX * ext;\n    const cp1y = p1y + segDirY * ext;\n    const cp2x = p2x - segDirX * ext;\n    const cp2y = p2y - segDirY * ext;\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cp1x,\n        cy0: cp1y,\n        cx1: cp1x + perpX * ext,\n        cy1: cp1y + perpY * ext,\n        x1: midX,\n        y1: midY\n      },\n      {\n        x0: midX,\n        y0: midY,\n        cx0: cp2x + perpX * ext,\n        cy0: cp2y + perpY * ext,\n        cx1: cp2x,\n        cy1: cp2y,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  } else {\n    const fromPrev = fromAttach.inward ?? {\n      x: fromEnd.x - (toStart.x - fromEnd.x),\n      y: fromEnd.y - (toStart.y - fromEnd.y)\n    };\n    const toNext = toAttach.inward ?? {\n      x: toStart.x - (fromEnd.x - toStart.x),\n      y: toStart.y - (fromEnd.y - toStart.y)\n    };\n    const dist = Math.hypot(p2x - p1x, p2y - p1y);\n    const tangentProj = (prev, at, towardX, towardY) => {\n      const dx = at.x - prev.x;\n      const dy = at.y - prev.y;\n      const len = Math.hypot(dx, dy);\n      const along = len === 0 ? 0 : (towardX * dx + towardY * dy) / len;\n      return Math.max(\n        0,\n        Math.min(dist * TANGENT_SPAN_FACTOR, MAX_TANGENT, along * 0.5)\n      );\n    };\n    const towardToX = toStart.x - fromEnd.x;\n    const towardToY = toStart.y - fromEnd.y;\n    const [cx1, cy1] = projectLine(\n      fromPrev.x,\n      fromPrev.y,\n      fromEnd.x,\n      fromEnd.y,\n      tangentProj(fromPrev, fromEnd, towardToX, towardToY)\n    );\n    const [cx2, cy2] = projectLine(\n      toNext.x,\n      toNext.y,\n      toStart.x,\n      toStart.y,\n      tangentProj(toNext, toStart, -towardToX, -towardToY)\n    );\n    const bulge = bypassed.length ? bowAround(p1x, p1y, p2x, p2y, bypassed, maxBow) : 0;\n    const chordLen = dist === 0 ? 1 : dist;\n    const ux = (p2x - p1x) / chordLen;\n    const uy = (p2y - p1y) / chordLen;\n    const bulgeX = -uy * bulge;\n    const bulgeY = ux * bulge;\n    const spreadX = ux * Math.abs(bulge);\n    const spreadY = uy * Math.abs(bulge);\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cx1 + bulgeX - spreadX,\n        cy0: cy1 + bulgeY - spreadY,\n        cx1: cx2 + bulgeX + spreadX,\n        cy1: cy2 + bulgeY + spreadY,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  }\n}\nfunction nearerEnd(segments, to) {\n  const start = segments[0];\n  const end = segments.at(-1);\n  return Math.hypot(start.x - to.x, start.y - to.y) < Math.hypot(end.x - to.x, end.y - to.y) ? \"start\" : \"end\";\n}\nfunction routedEdgeCurves(fromSegments, toSegments, route, sides) {\n  const fromAttach = attachment(\n    fromSegments,\n    sides?.from ?? nearerEnd(fromSegments, route[0])\n  );\n  const toAttach = attachment(\n    toSegments,\n    sides?.to ?? nearerEnd(toSegments, route.at(-1))\n  );\n  const points = [fromAttach.at, ...route, toAttach.at];\n  const tangent = (i) => {\n    const p = points[i];\n    const span = (q) => Math.hypot(q.x - p.x, q.y - p.y);\n    const along = (inward, next) => {\n      const len = inward ? span(inward) : 0;\n      const reach = span(next);\n      return len === 0 ? { x: next.x - p.x, y: next.y - p.y } : {\n        x: (p.x - inward.x) / len * reach,\n        y: (p.y - inward.y) / len * reach\n      };\n    };\n    if (i === 0) {\n      return along(fromAttach.inward, points[1]);\n    }\n    if (i === points.length - 1) {\n      const out = along(toAttach.inward, points[i - 1]);\n      return { x: -out.x, y: -out.y };\n    }\n    return {\n      x: (points[i + 1].x - points[i - 1].x) / 2,\n      y: (points[i + 1].y - points[i - 1].y) / 2\n    };\n  };\n  const curves = [];\n  for (let i = 0; i < points.length - 1; i++) {\n    const a = points[i];\n    const b = points[i + 1];\n    const ta = tangent(i);\n    const tb = tangent(i + 1);\n    curves.push({\n      x0: a.x,\n      y0: a.y,\n      cx0: a.x + ta.x / 3,\n      cy0: a.y + ta.y / 3,\n      cx1: b.x - tb.x / 3,\n      cy1: b.y - tb.y / 3,\n      x1: b.x,\n      y1: b.y\n    });\n  }\n  return curves;\n}\n\nexport {\n  svgPath,\n  projectLine,\n  curvePointAt,\n  curveMidpoint,\n  curveBounds,\n  dashCurves,\n  dashSpans,\n  slideAt,\n  slideCurves,\n  translateCurves,\n  ownStrand,\n  strandSides,\n  bowAround,\n  yToXOf,\n  PATH_RIBBON_SPACING_PX,\n  pathRibbonOffsets,\n  polylinePx,\n  selfLinkOf,\n  edgeJoinOf,\n  computeEdgeCurves,\n  routedEdgeCurves\n};\n", "// src/util/weakMemo.ts\nfunction weakMemo() {\n  const cache = /* @__PURE__ */ new WeakMap();\n  return (key, deps, compute) => {\n    const hit = cache.get(key);\n    if (hit?.deps.length === deps.length && hit.deps.every((d, i) => Object.is(d, deps[i]))) {\n      return hit.value;\n    }\n    const value = compute();\n    cache.set(key, { deps, value });\n    return value;\n  };\n}\n\nexport {\n  weakMemo\n};\n", "// src/overlayLabels.ts\nvar LABEL_PX = 11;\nvar LABEL_CHAR_PX = 6.2;\nvar LABEL_PAD = 4;\nfunction labelWidth(text) {\n  return text.length * LABEL_CHAR_PX + LABEL_PAD * 2;\n}\nfunction overlaps(a, b) {\n  return a.x0 < b.x1 && a.x1 > b.x0 && a.y0 < b.y1 && a.y1 > b.y0;\n}\nfunction offFrame(box, frame) {\n  return box.x1 <= 0 || box.x0 >= frame.width || box.y1 <= 0 || box.y0 >= frame.height;\n}\nfunction insideFrame(box, frame) {\n  return box.x0 >= 0 && box.x1 <= frame.width && box.y0 >= 0 && box.y1 <= frame.height;\n}\nfunction occupancy(frame, reserved = []) {\n  const placed = [...reserved];\n  return (box) => {\n    if (offFrame(box, frame) || placed.some((p) => overlaps(p, box))) {\n      return false;\n    }\n    placed.push(box);\n    return true;\n  };\n}\nfunction placeLabels(candidates, frame, take) {\n  const out = [];\n  const row = LABEL_PX + LABEL_PAD * 2;\n  const place = (c, text) => {\n    const w = labelWidth(text);\n    const direction = c.y > frame.height / 2 ? -1 : 1;\n    for (let tries = 0; tries <= (c.stack ?? 0); tries++) {\n      const y = c.y + direction * tries * row;\n      const box = {\n        x0: c.x - w / 2,\n        x1: c.x + w / 2,\n        y0: y - LABEL_PX - LABEL_PAD,\n        y1: y + LABEL_PAD\n      };\n      if (offFrame(box, frame)) {\n        return void 0;\n      }\n      if (insideFrame(box, frame) && (c.fits?.(box) ?? true) && take(box)) {\n        return { ...c, text, y, w };\n      }\n    }\n    return void 0;\n  };\n  for (const c of candidates) {\n    const placed = place(c, c.text) ?? (c.fallback === void 0 ? void 0 : place(c, c.fallback));\n    if (placed) {\n      out.push(placed);\n    }\n  }\n  return out;\n}\n\nexport {\n  LABEL_PX,\n  LABEL_CHAR_PX,\n  LABEL_PAD,\n  labelWidth,\n  overlaps,\n  occupancy,\n  placeLabels\n};\n", "import {\n  ownStrand,\n  strandSides\n} from \"./chunk-JJV2GT2Z.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/mergeRuns.ts\nfunction flip(strand) {\n  return strand === \"+\" ? \"-\" : \"+\";\n}\nfunction mergeRuns(graph, alone = /* @__PURE__ */ new Set()) {\n  const sides = graph.edges.map(strandSides);\n  const at = /* @__PURE__ */ new Map();\n  const attach = (id, side, ei) => {\n    pushTo(at, `${id}|${side}`, ei);\n  };\n  graph.edges.forEach((edge, ei) => {\n    attach(edge.from, sides[ei].from, ei);\n    attach(edge.to, sides[ei].to, ei);\n  });\n  const joinAfter = (a) => {\n    const out = at.get(`${a}|end`);\n    if (out?.length !== 1) {\n      return void 0;\n    }\n    const ei = out[0];\n    const edge = graph.edges[ei];\n    return edge.from === a && edge.to !== a && !alone.has(a) && !alone.has(edge.to) && sides[ei].from === \"end\" && sides[ei].to === \"start\" && at.get(`${edge.to}|start`)?.length === 1 ? ei : void 0;\n  };\n  const joined = /* @__PURE__ */ new Set();\n  const runOf = /* @__PURE__ */ new Map();\n  const runs = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const into = at.get(`${node.id}|start`);\n    const pred = into?.length === 1 ? graph.edges[into[0]].from : void 0;\n    if (runOf.has(node.id) || pred !== void 0 && joinAfter(pred) === into[0]) {\n      continue;\n    }\n    const run = [node.id];\n    for (; ; ) {\n      const ei = joinAfter(run.at(-1));\n      const next = ei === void 0 ? void 0 : graph.edges[ei].to;\n      if (next === void 0 || runOf.has(next)) {\n        break;\n      }\n      joined.add(ei);\n      run.push(next);\n    }\n    for (const id of run) {\n      runOf.set(id, node.id);\n    }\n    if (run.length > 1) {\n      runs.set(node.id, run);\n    }\n  }\n  for (const node of graph.nodes) {\n    if (!runOf.has(node.id)) {\n      runOf.set(node.id, node.id);\n    }\n  }\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const nodes = [];\n  for (const node of graph.nodes) {\n    if (runOf.get(node.id) !== node.id) {\n      continue;\n    }\n    const run = runs.get(node.id);\n    if (!run) {\n      nodes.push(node);\n      continue;\n    }\n    const members = run.map((id) => byId.get(id));\n    const backbone = members.filter(isBackbone);\n    const first = backbone.length ? backbone.reduce((a, b) => a.stable.start <= b.stable.start ? a : b) : members[0];\n    nodes.push({\n      id: node.id,\n      name: node.name,\n      length: members.reduce((sum, n) => sum + n.length, 0),\n      depth: node.depth,\n      stable: first.stable\n    });\n  }\n  const seen = /* @__PURE__ */ new Set();\n  const edges = [];\n  graph.edges.forEach((edge, ei) => {\n    const from = runOf.get(edge.from);\n    const to = runOf.get(edge.to);\n    const side = sides[ei];\n    const key = `${from}|${side.from}>${to}|${side.to}`;\n    if (joined.has(ei) || seen.has(key)) {\n      return;\n    }\n    seen.add(key);\n    edges.push({\n      from,\n      to,\n      ...side.from === \"start\" ? { fromStrand: flip(ownStrand(from)) } : {},\n      ...side.to === \"end\" ? { toStrand: flip(ownStrand(to)) } : {}\n    });\n  });\n  return {\n    graph: { ...graph, nodes, edges, paths: void 0, pathVisits: void 0 },\n    runs\n  };\n}\nfunction splitRuns(positions, runs, weightOf) {\n  const out = { ...positions };\n  for (const [id, members] of runs) {\n    const line = positions[id];\n    if (!line?.length) {\n      continue;\n    }\n    delete out[id];\n    const arc = arcPrefix(line);\n    const total = arc.at(-1);\n    const weights = members.map((m) => Math.max(weightOf(m), 0));\n    const weightSum = weights.reduce((a, b) => a + b, 0);\n    let from = 0;\n    members.forEach((member, k) => {\n      const share = weightSum ? weights[k] / weightSum * total : total / members.length;\n      const to = k === members.length - 1 ? total : from + share;\n      out[member] = slice(line, arc, from, to);\n      from = to;\n    });\n  }\n  return out;\n}\nfunction polylineSlice(line, from, to) {\n  if (line.length === 0) {\n    return [];\n  }\n  const arc = arcPrefix(line);\n  const total = arc.at(-1);\n  return slice(line, arc, from * total, to * total);\n}\nfunction polylineMidpoint(line) {\n  const arc = arcPrefix(line);\n  return pointAt(line, arc, arc.at(-1) / 2);\n}\nfunction arcPrefix(line) {\n  const arc = [0];\n  for (let i = 1; i < line.length; i++) {\n    arc.push(\n      arc[i - 1] + Math.hypot(line[i].x - line[i - 1].x, line[i].y - line[i - 1].y)\n    );\n  }\n  return arc;\n}\nfunction firstReaching(arc, s) {\n  let lo = 0;\n  let hi = arc.length;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (arc[mid] < s) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\nfunction pointAt(line, arc, s) {\n  if (s <= 0) {\n    return { ...line[0] };\n  }\n  const i = firstReaching(arc, s);\n  if (i >= arc.length) {\n    return { ...line.at(-1) };\n  }\n  const span = arc[i] - arc[i - 1];\n  const t = span > 0 ? (s - arc[i - 1]) / span : 0;\n  const a = line[i - 1];\n  const b = line[i];\n  return { x: a.x + (b.x - a.x) * t, y: a.y + (b.y - a.y) * t };\n}\nfunction slice(line, arc, from, to) {\n  const points = [pointAt(line, arc, from)];\n  for (let i = firstReaching(arc, from); i < line.length && arc[i] < to; i++) {\n    if (arc[i] > from) {\n      points.push({ ...line[i] });\n    }\n  }\n  points.push(pointAt(line, arc, to));\n  return points;\n}\n\nexport {\n  mergeRuns,\n  splitRuns,\n  polylineSlice,\n  polylineMidpoint\n};\n", "import {\n  pathOrigin,\n  trimOrigins\n} from \"./chunk-BRH73RCH.js\";\nimport {\n  PathVisitsBuilder\n} from \"./chunk-BEUTROKU.js\";\nimport {\n  isBackbone,\n  overlapsWindow\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/trimToWindow.ts\nfunction trimToWindow(graph, window) {\n  const inWindow = new Set(\n    graph.nodes.filter((n) => isBackbone(n) && overlapsWindow(n, window)).map((n) => n.id)\n  );\n  const paths = graph.paths ?? [];\n  if (inWindow.size === 0 || paths.length === 0) {\n    return graph;\n  }\n  const spans = paths.map((path) => {\n    let first = -1;\n    let last = -1;\n    path.nodeIds.forEach((id, i) => {\n      if (inWindow.has(id)) {\n        if (first < 0) {\n          first = i;\n        }\n        last = i;\n      }\n    });\n    return first < 0 ? void 0 : { first, last };\n  });\n  if (spans.every(\n    (span, i) => span?.first === 0 && span.last === paths[i].nodeIds.length - 1\n  )) {\n    return graph;\n  }\n  const kept = /* @__PURE__ */ new Set();\n  const trimmed = [];\n  const stretches = /* @__PURE__ */ new Map();\n  paths.forEach((path, i) => {\n    const span = spans[i];\n    if (span) {\n      const nodeIds = path.nodeIds.slice(span.first, span.last + 1);\n      for (const id of nodeIds) {\n        kept.add(id);\n      }\n      trimmed.push({ ...path, nodeIds });\n      stretches.set(path.name, { first: span.first, nodeIds });\n    }\n  });\n  return {\n    ...graph,\n    nodes: graph.nodes.filter((n) => kept.has(n.id)),\n    edges: graph.edges.filter((e) => kept.has(e.from) && kept.has(e.to)),\n    paths: trimmed,\n    pathVisits: graph.pathVisits && trimVisits(\n      graph.pathVisits,\n      paths,\n      spans,\n      new Map(graph.nodes.map((n) => [n.id, n.name]))\n    ),\n    anchorPaths: trimOrigins(graph, stretches)\n  };\n}\nfunction trimVisits(visits, paths, spans, nameOf) {\n  const next = visits.replay();\n  const out = new PathVisitsBuilder();\n  paths.forEach((path, p) => {\n    const origin = visits.pathIndex(pathOrigin(path.name).name);\n    const span = spans[p];\n    path.nodeIds.forEach((id, i) => {\n      const segment = nameOf.get(id) ?? id;\n      const at = next(visits.slot(segment), origin);\n      if (at >= 0 && span && i >= span.first && i <= span.last) {\n        out.add(\n          segment,\n          visits.paths[origin],\n          visits.samples[origin],\n          visits.start[at],\n          visits.reversed[at] === 1\n        );\n      }\n    });\n  });\n  return out.build();\n}\nfunction clipToWindow(graph, window, reachBp) {\n  const nodes = graph.nodes.map((node) => {\n    if (!isBackbone(node)) {\n      return node;\n    }\n    const from = node.stable.start;\n    const to = from + node.length;\n    const [start, end] = overlapsWindow(node, window) ? [Math.max(from, window.start), Math.min(to, window.end)] : to <= window.start ? [Math.max(from, to - reachBp), to] : [from, Math.min(to, from + reachBp)];\n    return start === from && end === to ? node : {\n      ...node,\n      length: end - start,\n      stable: { ...node.stable, start },\n      unclipped: { start: from, length: node.length }\n    };\n  });\n  return nodes.some((node, i) => node !== graph.nodes[i]) ? { ...graph, nodes } : graph;\n}\nfunction unclipped(graph) {\n  return graph.nodes.some((n) => n.unclipped) ? {\n    ...graph,\n    nodes: graph.nodes.map(\n      ({ unclipped: full, ...node }) => full && node.stable ? {\n        ...node,\n        length: full.length,\n        stable: { ...node.stable, start: full.start }\n      } : node\n    )\n  } : graph;\n}\n\nexport {\n  trimToWindow,\n  clipToWindow,\n  unclipped\n};\n", "import {\n  unclipped\n} from \"./chunk-H4UHV22B.js\";\nimport {\n  referenceVisitStarts\n} from \"./chunk-BRH73RCH.js\";\nimport {\n  computeEdgeCurves,\n  edgeJoinOf,\n  routedEdgeCurves,\n  strandSides\n} from \"./chunk-JJV2GT2Z.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  firstNodeAtOrAfter,\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/deletionEdges.ts\nvar MIN_DELETION_BP = 1;\nvar deletionKey = (reference) => `skips ${reference ?? \"the reference\"} sequence (a deletion)`;\nfunction bypassedPoints(nodePositions, bypassed) {\n  return bypassed.flatMap((id) => nodePositions[id] ?? []);\n}\nfunction edgeCurvesOf(nodePositions, edge, axis, bypassed, route, stranded) {\n  const from = nodePositions[edge.from];\n  const to = nodePositions[edge.to];\n  if (!from?.length || !to?.length) {\n    return void 0;\n  }\n  return route ? routedEdgeCurves(\n    from,\n    to,\n    route,\n    stranded ? strandSides(edge) : void 0\n  ) : computeEdgeCurves(\n    from,\n    to,\n    edgeJoinOf(edge, stranded),\n    axis,\n    bypassed ? bypassedPoints(nodePositions, bypassed) : []\n  );\n}\nfunction backboneBySequence(graph) {\n  const bySequence = groupBy(\n    graph.nodes.filter(isBackbone),\n    (node) => node.stable.refName\n  );\n  for (const list of bySequence.values()) {\n    list.sort((a, b) => a.stable.start - b.stable.start);\n  }\n  return bySequence;\n}\nfunction bypassedNodes(nodes, start, end) {\n  const bypassed = [];\n  if (nodes) {\n    for (let i = firstNodeAtOrAfter(nodes, start); i < nodes.length; i++) {\n      const node = nodes[i];\n      if (node.stable.start >= end) {\n        break;\n      }\n      if (node.stable.start + node.length <= end) {\n        bypassed.push(node.id);\n      }\n    }\n  }\n  return bypassed;\n}\nfunction skipsBetween(edge, from, to, forwards) {\n  const { fromStrand, toStrand } = edge;\n  if (fromStrand === void 0 || toStrand === void 0) {\n    return true;\n  }\n  const leavesRight = fromStrand === (from.stable.strand ?? \"+\");\n  const arrivesLeft = toStrand === (to.stable.strand ?? \"+\");\n  return forwards ? leavesRight && arrivesLeft : !leavesRight && !arrivesLeft;\n}\nfunction skippedSpan(edge, from, to, startsOf) {\n  let best;\n  for (const a of startsOf(from)) {\n    for (const b of startsOf(to)) {\n      const forwards = a <= b;\n      const span = forwards ? { start: a + from.length, end: b } : { start: b + to.length, end: a };\n      if (skipsBetween(edge, from, to, forwards) && (!best || Math.abs(span.end - span.start) < Math.abs(best.end - best.start))) {\n        best = span;\n      }\n    }\n  }\n  return best;\n}\nvar COPY_SWITCH_SHARE = 0.01;\nfunction repeatCopies(backbone, startsOf) {\n  const bySequence = /* @__PURE__ */ new Map();\n  for (const [refName, nodes] of backbone) {\n    const copies = nodes.flatMap((node) => {\n      const starts = startsOf(node);\n      return starts.slice(1).map((next, i) => ({\n        at: starts[i],\n        copy: next - starts[i]\n      }));\n    });\n    if (copies.length) {\n      bySequence.set(\n        refName,\n        copies.sort((a, b) => a.at - b.at)\n      );\n    }\n  }\n  return bySequence;\n}\nfunction switchesCopy(copies, start, bp) {\n  if (!copies) {\n    return false;\n  }\n  const i = partitionPoint(copies.length, (k) => copies[k].at < start);\n  const near = [copies[i - 1], copies[i]].filter((c) => c !== void 0).sort((a, b) => Math.abs(a.at - start) - Math.abs(b.at - start))[0];\n  return near !== void 0 && Math.abs(near.at - start) <= near.copy && Math.abs(bp - near.copy) <= near.copy * COPY_SWITCH_SHARE;\n}\nfunction deletionEdges(cut) {\n  const graph = unclipped(cut);\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const backbone = backboneBySequence(graph);\n  const startsOf = referenceVisitStarts(graph);\n  const copies = repeatCopies(backbone, startsOf);\n  const found = [];\n  for (let edgeIndex = 0; edgeIndex < graph.edges.length; edgeIndex++) {\n    const edge = graph.edges[edgeIndex];\n    const from = byId.get(edge.from);\n    const to = byId.get(edge.to);\n    if (!edge.foldBridge && from !== void 0 && to !== void 0 && isBackbone(from) && isBackbone(to) && from.stable.refName === to.stable.refName) {\n      const span = skippedSpan(edge, from, to, startsOf);\n      const refName = from.stable.refName;\n      const bp = span ? span.end - span.start : 0;\n      if (span && bp >= MIN_DELETION_BP && !switchesCopy(copies.get(refName), span.start, bp)) {\n        const { start, end } = span;\n        found.push({\n          edgeIndex,\n          from: edge.from,\n          to: edge.to,\n          ...edge.fromStrand ? { fromStrand: edge.fromStrand } : {},\n          ...edge.toStrand ? { toStrand: edge.toStrand } : {},\n          refName,\n          start,\n          end,\n          bp,\n          bypassed: bypassedNodes(backbone.get(refName), start, end)\n        });\n      }\n    }\n  }\n  return found;\n}\nfunction closableDeletions(graph, deletions) {\n  const parent = /* @__PURE__ */ new Map();\n  const root = (id) => {\n    let r = id;\n    while (parent.has(r)) {\n      r = parent.get(r);\n    }\n    if (r !== id) {\n      parent.set(id, r);\n    }\n    return r;\n  };\n  const join = (a, b) => {\n    const [ra, rb] = [root(a), root(b)];\n    if (ra !== rb) {\n      parent.set(ra, rb);\n    }\n    return ra !== rb;\n  };\n  const candidates = new Set(deletions.map((d) => d.edgeIndex));\n  graph.edges.forEach((e, ei) => {\n    if (!candidates.has(ei)) {\n      join(e.from, e.to);\n    }\n  });\n  return new Set(\n    deletions.filter((d) => !join(d.from, d.to)).map((d) => d.edgeIndex)\n  );\n}\nvar drawings = /* @__PURE__ */ new WeakMap();\nfunction deletionDrawing(graph, deletions, show = true) {\n  let byShow = drawings.get(deletions);\n  if (!byShow) {\n    byShow = /* @__PURE__ */ new Map();\n    drawings.set(deletions, byShow);\n  }\n  let drawing = byShow.get(show);\n  if (!drawing) {\n    const hidden = show ? /* @__PURE__ */ new Set() : closableDeletions(graph, deletions);\n    drawing = {\n      shown: deletions.filter((d) => !hidden.has(d.edgeIndex)),\n      bypassed: new Map(deletions.map((d) => [d.edgeIndex, d.bypassed])),\n      hidden\n    };\n    byShow.set(show, drawing);\n  }\n  return drawing;\n}\n\nexport {\n  deletionKey,\n  edgeCurvesOf,\n  deletionEdges,\n  closableDeletions,\n  deletionDrawing\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  labelWidth,\n  occupancy\n} from \"./chunk-AB35TJST.js\";\nimport {\n  polylineMidpoint\n} from \"./chunk-HNNP5QUN.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-T35SFBHW.js\";\nimport {\n  curveBounds,\n  curveMidpoint,\n  polylinePx\n} from \"./chunk-JJV2GT2Z.js\";\n\n// src/graphLabels.ts\nvar MIN_DELETION_LABEL_PX = 26;\nvar PX_PER_NODE_LABEL = 4e4;\nvar MIN_NODE_LABELS = 8;\nvar LEADER_GAP_PX = 8;\nvar LABEL_CHAR_PX = 5.7;\nvar LABEL_PAD_PX = 6;\nvar LABEL_HEIGHT_PX = 13;\nvar LABEL_GAP_PX = 3;\nvar MAX_LABEL_OVERHANG = 2;\nfunction labelHalfWidth(text) {\n  return (text.length * LABEL_CHAR_PX + LABEL_PAD_PX + LABEL_GAP_PX) / 2;\n}\nvar LABEL_HALF_HEIGHT = (LABEL_HEIGHT_PX + LABEL_GAP_PX) / 2;\nvar MIN_LABEL_HALF_WIDTH = labelHalfWidth(\"1 bp\");\nfunction boxAt(halfW, x, y) {\n  return {\n    x0: x - halfW,\n    x1: x + halfW,\n    y0: y - LABEL_HALF_HEIGHT,\n    y1: y + LABEL_HALF_HEIGHT\n  };\n}\nfunction rowLabelBox(text, screenY) {\n  return {\n    x0: 6,\n    x1: 6 + labelWidth(text) + LABEL_GAP_PX,\n    y0: screenY - 8 - LABEL_GAP_PX / 2,\n    y1: screenY + 8 + LABEL_GAP_PX / 2\n  };\n}\nfunction clamp(v, lo, hi) {\n  return hi < lo ? v : Math.min(Math.max(v, lo), hi);\n}\nfunction groupDigits(n) {\n  return String(n).replace(/\\B(?=(\\d{3})+$)/g, \",\");\n}\nfunction formatBp(bp) {\n  const [value, unit] = bp >= 999500 ? [bp / 1e6, \"Mb\"] : bp >= 1e3 ? [bp / 1e3, \"kb\"] : [];\n  if (value === void 0) {\n    return `${bp} bp`;\n  }\n  return `${+value.toFixed(value >= 100 ? 0 : 1)} ${unit}`;\n}\nfunction deletionText(bp) {\n  return `${formatBp(bp)} del`;\n}\nfunction arcOutward(curves, apex, scaleX, scaleY) {\n  const first = curves[0];\n  const last = curves[curves.length - 1];\n  const dx = (apex.x - (first.x0 + last.x1) / 2) * scaleX;\n  const dy = (apex.y - (first.y0 + last.y1) / 2) * scaleY;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? { x: 0, y: -1 } : { x: dx / len, y: dy / len };\n}\nfunction boxSupport(box, dir) {\n  return Math.abs(dir.x) * (box.x1 - box.x0) / 2 + Math.abs(dir.y) * (box.y1 - box.y0) / 2;\n}\nfunction boxRayCrossing(box, dir) {\n  const halfW = (box.x1 - box.x0) / 2;\n  const halfH = (box.y1 - box.y0) / 2;\n  return Math.min(\n    dir.x === 0 ? Infinity : halfW / Math.abs(dir.x),\n    dir.y === 0 ? Infinity : halfH / Math.abs(dir.y)\n  );\n}\nfunction runBounds(nodeIds, nodePositions) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const id of nodeIds) {\n    for (const p of nodePositions[id] ?? []) {\n      minX = Math.min(minX, p.x);\n      maxX = Math.max(maxX, p.x);\n      minY = Math.min(minY, p.y);\n      maxY = Math.max(maxY, p.y);\n    }\n  }\n  return minX === Infinity ? void 0 : { minX, minY, maxX, maxY };\n}\nvar nodeOrderCache = weakMemo();\nfunction labelOrder(nodePositions, nodeLengths) {\n  return nodeOrderCache(\n    nodePositions,\n    [nodeLengths],\n    () => Object.entries(nodePositions).filter(([id, segments]) => segments.length > 0 && nodeLengths.has(id)).sort(([a], [b]) => nodeLengths.get(b) - nodeLengths.get(a))\n  );\n}\nvar arcCache = weakMemo();\nfunction arcPlacements(nodePositions, deletions, axis, version, routes, stranded) {\n  const { scaleX, scaleY } = axis;\n  return arcCache(\n    nodePositions,\n    [deletions, routes, stranded, scaleX, scaleY, version],\n    () => {\n      const arcs = [];\n      for (const deletion of [...deletions].sort((a, b) => b.bp - a.bp)) {\n        const curves = edgeCurvesOf(\n          nodePositions,\n          deletion,\n          axis,\n          deletion.bypassed,\n          routes?.[deletion.edgeIndex],\n          stranded\n        );\n        const apex = curves ? curveMidpoint(curves) : void 0;\n        if (curves && apex) {\n          const { minX, minY, maxX, maxY } = curveBounds(curves);\n          arcs.push({\n            deletion,\n            curves,\n            apex,\n            // in screen px, so the two axes' units cannot be added by accident\n            extent: Math.max((maxX - minX) * scaleX, (maxY - minY) * scaleY)\n          });\n        }\n      }\n      return arcs;\n    }\n  );\n}\nfunction sizeLabelCandidates({\n  nodePositions,\n  nodeLengths,\n  deletions,\n  deletionRoutes,\n  stranded = false,\n  alleleDeletions,\n  axis,\n  translateX,\n  translateY,\n  width,\n  height,\n  version = 0\n}) {\n  const { scaleX, scaleY } = axis;\n  const deletionCandidates = [];\n  const nodeCandidates = [];\n  for (const { deletion, curves, apex, extent } of arcPlacements(\n    nodePositions,\n    deletions,\n    axis,\n    version,\n    deletionRoutes,\n    stranded\n  )) {\n    if (extent >= MIN_DELETION_LABEL_PX) {\n      const text = deletionText(deletion.bp);\n      const halfW = labelHalfWidth(text);\n      const box = boxAt(halfW, 0, 0);\n      const arcX = apex.x * scaleX + translateX;\n      const arcY = apex.y * scaleY + translateY;\n      if (arcX < 0 || arcX > width || arcY < 0 || arcY > height) {\n        continue;\n      }\n      const fits = extent >= halfW * 2 / MAX_LABEL_OVERHANG;\n      const bow = arcOutward(curves, apex, scaleX, scaleY);\n      const offset = boxSupport(box, bow) + LEADER_GAP_PX;\n      const x = fits ? arcX : clamp(arcX + bow.x * offset, halfW, width - halfW);\n      const y = fits ? arcY : clamp(\n        arcY + bow.y * offset,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      const away = Math.hypot(x - arcX, y - arcY);\n      let leader;\n      if (away > 0) {\n        const dir = { x: (x - arcX) / away, y: (y - arcY) / away };\n        const crossing = boxRayCrossing(box, dir);\n        leader = {\n          arcX,\n          arcY,\n          labelX: x - dir.x * crossing,\n          labelY: y - dir.y * crossing\n        };\n      }\n      deletionCandidates.push({\n        label: {\n          key: `del:${deletion.edgeIndex}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\",\n          leader\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  const labelledByDeletion = /* @__PURE__ */ new Set();\n  const alleleRuns = [...alleleDeletions ?? []].sort((a, b) => b.bp - a.bp);\n  for (const run of alleleRuns) {\n    const drawn = runBounds(run.nodeIds, nodePositions);\n    if (!drawn) {\n      continue;\n    }\n    const shownLeft = Math.max(drawn.minX * scaleX + translateX, 0);\n    const shownRight = Math.min(drawn.maxX * scaleX + translateX, width);\n    const shownTop = Math.max(drawn.minY * scaleY + translateY, 0);\n    const shownBottom = Math.min(drawn.maxY * scaleY + translateY, height);\n    if (shownRight < shownLeft || shownBottom < shownTop) {\n      continue;\n    }\n    const extent = Math.max(shownRight - shownLeft, shownBottom - shownTop);\n    const text = deletionText(run.bp);\n    const halfW = labelHalfWidth(text);\n    if (extent >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      for (const id of run.nodeIds) {\n        labelledByDeletion.add(id);\n      }\n      const x = clamp((shownLeft + shownRight) / 2, halfW, width - halfW);\n      const y = clamp(\n        (shownTop + shownBottom) / 2,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      deletionCandidates.push({\n        label: {\n          key: `alleledel:${run.nodeIds.join(\",\")}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\"\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  for (const [id, segments] of labelOrder(nodePositions, nodeLengths)) {\n    if (labelledByDeletion.has(id)) {\n      continue;\n    }\n    const { x, y } = polylineMidpoint(segments);\n    const screenY = y * scaleY + translateY;\n    if (screenY + LABEL_HALF_HEIGHT <= 0 || screenY - LABEL_HALF_HEIGHT >= height) {\n      continue;\n    }\n    const drawn = polylinePx(segments, scaleX, scaleY);\n    if (drawn < MIN_LABEL_HALF_WIDTH * 2 / MAX_LABEL_OVERHANG) {\n      continue;\n    }\n    const text = formatBp(nodeLengths.get(id));\n    const halfW = labelHalfWidth(text);\n    if (drawn >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      const screenX = x * scaleX + translateX;\n      nodeCandidates.push({\n        label: {\n          key: `node:${id}`,\n          text,\n          x: screenX,\n          y: screenY,\n          kind: \"node\"\n        },\n        box: boxAt(halfW, screenX, screenY)\n      });\n    }\n  }\n  return { deletions: deletionCandidates, nodes: nodeCandidates };\n}\nfunction nodeLabelBudget(width, height) {\n  return Math.max(\n    MIN_NODE_LABELS,\n    Math.floor(width * height / PX_PER_NODE_LABEL)\n  );\n}\nfunction placeSizeLabels(candidates, take, budget = Infinity) {\n  const labels = [];\n  for (const { label, box } of candidates) {\n    if (labels.length >= budget) {\n      break;\n    }\n    if (take(box)) {\n      labels.push(label);\n    }\n  }\n  return labels;\n}\nfunction graphLabels({\n  reserved,\n  take,\n  ...args\n}) {\n  take ??= occupancy(args, reserved);\n  const { deletions, nodes } = sizeLabelCandidates(args);\n  return [\n    ...placeSizeLabels(deletions, take),\n    ...placeSizeLabels(nodes, take, nodeLabelBudget(args.width, args.height))\n  ];\n}\n\nexport {\n  rowLabelBox,\n  groupDigits,\n  formatBp,\n  sizeLabelCandidates,\n  nodeLabelBudget,\n  placeSizeLabels,\n  graphLabels\n};\n", "import {\n  groupDigits\n} from \"./chunk-X4IP4DAD.js\";\nimport {\n  pathOrigin\n} from \"./chunk-BRH73RCH.js\";\nimport {\n  isGenericSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathColors.ts\nfunction nameHue(name) {\n  let hash = 0;\n  for (let i = 0; i < name.length; i++) {\n    hash = name.charCodeAt(i) + ((hash << 5) - hash);\n  }\n  return Math.abs(hash % 360);\n}\nfunction pathHueAt(index, count) {\n  return index * 360 / count;\n}\nvar PATH_SATURATION = 0.7;\nvar PATH_LIGHTNESS = 0.5;\nvar MAX_PATH_COLORS = 16;\nfunction pathColorsLegible(pathCount) {\n  return pathCount > 0 && pathCount <= MAX_PATH_COLORS;\n}\nfunction pathCssColor(index, count) {\n  return `hsl(${pathHueAt(index, count)}, ${PATH_SATURATION * 100}%, ${PATH_LIGHTNESS * 100}%)`;\n}\nfunction pathGreyCssColor(index, count) {\n  const lightness = count > 1 ? 25 + 45 * index / (count - 1) : 45;\n  return `hsl(0, 0%, ${lightness}%)`;\n}\nfunction labelTiers(name) {\n  const parts = pathOrigin(name).name.split(\"#\");\n  const full = parts.join(\"#\");\n  if (parts.length >= 3 && isGenericSample(parts[0])) {\n    const contig = parts.slice(2).join(\"#\");\n    return [contig, contig, full];\n  }\n  return [parts[0], parts.slice(0, 2).join(\"#\"), full];\n}\nfunction offsetTiers(name, tiers) {\n  const { start } = pathOrigin(name);\n  return tiers.map((t) => `${t} @${groupDigits(start)}`);\n}\nfunction pathLegend(paths, colors) {\n  const firstOf = /* @__PURE__ */ new Map();\n  paths.forEach((path, i) => {\n    if (!firstOf.has(path.name)) {\n      firstOf.set(path.name, i);\n    }\n  });\n  const entries = [...firstOf].map(([name2, i]) => ({ name: name2, i }));\n  const named = entries.map((e) => labelTiers(e.name));\n  const name = (t) => entries.map((_, k) => named[k][t]);\n  const offset = (t) => entries.map((e, k) => offsetTiers(e.name, named[k])[t]);\n  const candidates = [\n    name(0),\n    name(1),\n    offset(0),\n    name(2),\n    offset(1),\n    offset(2)\n  ];\n  const distinct = candidates.find(\n    (labels2) => new Set(labels2).size === entries.length\n  );\n  const labels = distinct ?? candidates.at(-1);\n  return entries.map(({ name: name2, i }, k) => ({\n    name: name2,\n    label: labels[k],\n    color: colors?.[i] ?? pathCssColor(i, paths.length)\n  }));\n}\nfunction walkLabelsOf(entries) {\n  const seen = /* @__PURE__ */ new Map();\n  return new Map(\n    [...entries].sort((a, b) => a.label.localeCompare(b.label)).map((e) => {\n      const n = (seen.get(e.label) ?? 0) + 1;\n      seen.set(e.label, n);\n      return [e.name, n > 1 ? `${e.label} (${n})` : e.label];\n    })\n  );\n}\n\nexport {\n  nameHue,\n  pathHueAt,\n  PATH_SATURATION,\n  PATH_LIGHTNESS,\n  MAX_PATH_COLORS,\n  pathColorsLegible,\n  pathCssColor,\n  pathGreyCssColor,\n  pathLegend,\n  walkLabelsOf\n};\n", "import {\n  panSNHaplotype\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/nodeWidths.ts\nvar NODE_WIDTHS = [\n  {\n    value: \"depth\",\n    label: \"By depth\",\n    description: \"Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform.\"\n  },\n  {\n    value: \"frequency\",\n    label: \"By frequency\",\n    description: \"As wide as the share of haplotypes that pass a node, or its AF tag: full width at 100%, half at 50%, and wider where a haplotype passes it more than once.\"\n  },\n  {\n    value: \"uniform\",\n    label: \"Uniform\",\n    description: \"Every node the same thickness.\"\n  }\n];\nvar MIN_FACTOR = 0.3;\nvar MAX_FACTOR = 3;\nvar MIN_FREQUENCY_FACTOR = 0.05;\nfunction meanDepth(graph) {\n  let weighted = 0;\n  let length = 0;\n  for (const node of graph.nodes) {\n    weighted += node.depth * node.length;\n    length += node.length;\n  }\n  return length > 0 ? weighted / length : 0;\n}\nfunction haplotypeOf(path) {\n  return path.sample === void 0 ? panSNHaplotype(path.name) ?? path.name : `${path.sample}#${path.haplotype ?? 0}`;\n}\nfunction haplotypeCount(graph) {\n  return new Set((graph.paths ?? []).map(haplotypeOf)).size;\n}\nfunction nodeFrequency(node, haplotypes) {\n  return node.frequency ?? (haplotypes > 0 ? node.depth / haplotypes : void 0);\n}\nfunction withFrequencies(graph, frequencies) {\n  if (!frequencies) {\n    return graph;\n  }\n  const nodes = graph.nodes.map((node) => {\n    const frequency = frequencies[node.name];\n    return frequency === void 0 ? node : { ...node, frequency };\n  });\n  return { ...graph, nodes };\n}\nfunction widthNorm(graph, nodeWidth) {\n  return nodeWidth === \"depth\" ? meanDepth(graph) : nodeWidth === \"frequency\" ? haplotypeCount(graph) : 0;\n}\nfunction frequencyFactor(f) {\n  return Math.min(MAX_FACTOR, Math.max(MIN_FREQUENCY_FACTOR, f));\n}\nfunction frequencyWidthFactor(node, haplotypes) {\n  const f = nodeFrequency(node, haplotypes);\n  return f === void 0 ? 1 : frequencyFactor(f);\n}\nfunction frequencyKey(contigThickness) {\n  return [1, 0.5, 0.1].map((f) => ({\n    label: `${f * 100}%`,\n    widthPx: contigThickness * frequencyFactor(f)\n  }));\n}\nfunction depthWidthFactor(node, mean) {\n  if (!(mean > 0) || !(node.depth > 0)) {\n    return 1;\n  }\n  return Math.min(\n    MAX_FACTOR,\n    Math.max(MIN_FACTOR, Math.sqrt(node.depth / mean))\n  );\n}\nfunction nodeWidthPx(node, contigThickness, nodeWidth, norm) {\n  return contigThickness * (nodeWidth === \"depth\" ? depthWidthFactor(node, norm) : nodeWidth === \"frequency\" ? frequencyWidthFactor(node, norm) : 1);\n}\nfunction maxNodeWidthPx(contigThickness, nodeWidth) {\n  return contigThickness * (nodeWidth === \"uniform\" ? 1 : MAX_FACTOR);\n}\nvar MIN_WALK_LANE_PX = 4;\nfunction walkLaneWidthPx(width, lanes) {\n  return Math.max(width / lanes, MIN_WALK_LANE_PX);\n}\nfunction nodeInk(graph, nodeById, contigThickness, nodeWidth, lanes = 0) {\n  const norm = graph ? widthNorm(graph, nodeWidth) : 0;\n  const reach = (width) => lanes > 0 ? walkLaneWidthPx(width, lanes) * lanes / 2 : width / 2;\n  return {\n    maxHalfWidthPx: reach(maxNodeWidthPx(contigThickness, nodeWidth)),\n    halfWidthPx: (id) => {\n      const node = nodeById?.get(id);\n      return reach(\n        node ? nodeWidthPx(node, contigThickness, nodeWidth, norm) : contigThickness\n      );\n    }\n  };\n}\n\nexport {\n  NODE_WIDTHS,\n  meanDepth,\n  haplotypeCount,\n  nodeFrequency,\n  withFrequencies,\n  widthNorm,\n  frequencyKey,\n  nodeWidthPx,\n  maxNodeWidthPx,\n  walkLaneWidthPx,\n  nodeInk\n};\n", "// src/edgeWidths.ts\nvar EDGE_WIDTHS = [\n  {\n    value: \"uniform\",\n    label: \"Uniform\",\n    description: \"Every link the same thickness.\"\n  },\n  {\n    value: \"walks\",\n    label: \"By walks\",\n    description: \"Thicker the more walks take a link, on the square root of its count against the busiest link in the cut. A graph without walks draws uniform.\"\n  }\n];\nvar MIN_FACTOR = 0.5;\nvar MAX_FACTOR = 4;\nfunction busiestEdge(graph) {\n  let most = 0;\n  for (const edge of graph.edges) {\n    most = Math.max(most, edge.pathIds?.length ?? 0);\n  }\n  return most;\n}\nfunction edgeWidthFactor(walks, busiest, edgeWidth) {\n  if (edgeWidth === \"uniform\" || busiest === 0) {\n    return 1;\n  }\n  return MIN_FACTOR + (MAX_FACTOR - MIN_FACTOR) * Math.sqrt(walks / busiest);\n}\n\nexport {\n  EDGE_WIDTHS,\n  busiestEdge,\n  edgeWidthFactor\n};\n"],
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package/dist/chunks/{chunk-BJHWGRMP.js → chunk-PEE2MP7K.js}

@@ -1,2 +1,2 @@
 function o(t){return t===void 0||t==="*"?void 0:t}function s(t){let e=t.split("	");return{refName:e[0],start:+e[1],end:+e[2],segmentCount:+e[3],pathCount:+e[4],inversion:e[5]==="1",shortestAlleleLength:+e[6],longestAlleleLength:+e[7],segments:e[11],shortestAllele:o(e[12]),longestAllele:o(e[13])}}function u(t,e){return t.key!==void 0||e.key!==void 0?t.key===e.key:t.refName===e.refName&&t.start===e.start&&t.end===e.end}function i(t){return t.key??`${t.refName}:${t.start}-${t.end}`}function b(t){let{shortestAlleleLength:e,longestAlleleLength:n}=t;return e===n?`${n.toLocaleString()} bp`:`${e.toLocaleString()}-${n.toLocaleString()} bp`}var r=2147483647;function a(t){let{pathCount:e,segmentCount:n,inversion:l}=t;return[`${n} segments`,e===r?"more paths than gfatools counts":`up to ${e.toLocaleString()} paths`,...l?["inversion"]:[]].join(", ")}export{s as a,u as b,i as c,b as d,r as e,a as f};
-//# sourceMappingURL=chunk-BJHWGRMP.js.map
+//# sourceMappingURL=chunk-PEE2MP7K.js.map

package/dist/chunks/{chunk-BJHWGRMP.js.map → chunk-PEE2MP7K.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FX4RDMDN.js"],
   "sourcesContent": ["// src/bubbles/bubbleLine.ts\nfunction sequence(field) {\n  return field === void 0 || field === \"*\" ? void 0 : field;\n}\nfunction parseBubbleLine(line) {\n  const cols = line.split(\"\t\");\n  return {\n    refName: cols[0],\n    start: +cols[1],\n    end: +cols[2],\n    segmentCount: +cols[3],\n    pathCount: +cols[4],\n    inversion: cols[5] === \"1\",\n    shortestAlleleLength: +cols[6],\n    longestAlleleLength: +cols[7],\n    segments: cols[11],\n    shortestAllele: sequence(cols[12]),\n    longestAllele: sequence(cols[13])\n  };\n}\nfunction sameBubble(a, b) {\n  return a.key !== void 0 || b.key !== void 0 ? a.key === b.key : a.refName === b.refName && a.start === b.start && a.end === b.end;\n}\nfunction bubbleKey(b) {\n  return b.key ?? `${b.refName}:${b.start}-${b.end}`;\n}\nfunction bubbleLabel(bubble) {\n  const { shortestAlleleLength: min, longestAlleleLength: max } = bubble;\n  return min === max ? `${max.toLocaleString()} bp` : `${min.toLocaleString()}-${max.toLocaleString()} bp`;\n}\nvar SATURATED_PATH_COUNT = 2147483647;\nfunction bubbleDescription(bubble) {\n  const { pathCount, segmentCount, inversion } = bubble;\n  return [\n    `${segmentCount} segments`,\n    pathCount === SATURATED_PATH_COUNT ? \"more paths than gfatools counts\" : `up to ${pathCount.toLocaleString()} paths`,\n    ...inversion ? [\"inversion\"] : []\n  ].join(\", \");\n}\n\nexport {\n  parseBubbleLine,\n  sameBubble,\n  bubbleKey,\n  bubbleLabel,\n  SATURATED_PATH_COUNT,\n  bubbleDescription\n};\n"],
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   "names": ["sequence", "field", "parseBubbleLine", "line", "cols", "sameBubble", "a", "b", "bubbleKey", "bubbleLabel", "bubble", "min", "max", "SATURATED_PATH_COUNT", "bubbleDescription", "pathCount", "segmentCount", "inversion"]

package/dist/chunks/{chunk-T2VC3EEL.js → chunk-PMM6BEKY.js}

@@ -1,2 +1,2 @@
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